Mountain- and brown hare genetic polymorphisms to survey local adaptations and conservation status of the heath hare (Lepus timidus sylvaticus, Nilsson 1831)

We provide the first whole genome sequences from three specimens of the mountain hare subspecies the heath hare (Lepus timidus sylvaticus), along with a sample subset of two mountain hares (Lepus timidus timidus) and two brown hares (Lepus europaeus) from Sweden. The heath hare has a unique grey winter pelage as compared to other mountain hares (white) and brown hares (mostly brown), and face regional extinction, likely due to competitive exclusion from the non-native brown hare. Whole genome resequencing from the eight hare specimens was mapped to the Lepus timidus pseudoreference genome and used for detection of 11,363,883 polymorphic nucleotide positions. We show that genomic data can be useful for addressing local adaptations and conservation status of mountain hares and brown hares in Sweden, including unique subspecies.The genomic data described could be used to assess adaptations of hares in for example pigmentation, cold durability and pathogen resistance in local, regional or distribution-wide range. A particular value is to develop an integrated monitoring tool for assessing the conservation status of the heath hare in southern and central Sweden. This could be done by integrating genetic data, harvest data, pellet inventories and camera trapping. In addition to general conservation, the long-term preservation of the heath hare, as well as understanding of the nature of interactions between mountain hares and brown hares, is important from a resource perceptive since hares are a game species in Sweden and elsewhere and, as such, a source of meat and recreation.Funding provided by: Swedish Environmental Protection AgencyCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100004357Award Number: NV-05813-21Muscle tissue samples were obtained from hares shot from 2005-2017 during the regular hunting season in Sweden. A single 350 bp fragment sized Illumina TruSeq PCR free library (Illumina, USA) was prepared for each hare sample at the SciLifeLab in Stockholm, Sweden (National Genomics Infrastructure Stockholm, Sweden). The samples were then pooled in equimolar ratios and sequenced over 4 lanes on the Illumina HiSeqX platform using the 2 X 151 Hiseq X SBS chemistry. The Bcl to FastQ conversion was performed using bcl2fastq_v2.19.1.403 of the Illumina software package CASAVA. The trimmed reads were then mapped to the psedudoreference Lepus timidus genome (NCBI accession: GCA_009760805.1) with the Burrows Wheeler Aligner, BWA version 0.7.17 using default the settings for the bwa mem algorithm. Raw variants were called across the genome in 100,000 bp regions using freebayes version 1.3.1